runSeuratIntegration: Run Seurat integration

In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

Run Seurat integration

Description

Run Seurat integration

Usage

runSeuratIntegration(
  object,
  Seurat.metadata = "",
  Seurat.split.by = "",
  n.dims.use = 30,
  Seurat.variablegenes.method = "vst",
  Seurat.variablegenes.number = 2000,
  use.SingCellaR.varGenes = F,
  k.anchor = 5,
  k.filter = 200,
  k.score = 30
)

Arguments

object	The SingCellaR object.
Seurat.metadata	cell metadata (a data frame format)
Seurat.split.by	The indicated feature for splitting samples for the integration.
n.dims.use	The number of PCA dimensions used for the input for Seurat.
Seurat.variablegenes.method	The method for variable genes selection. Default 'vst'
Seurat.variablegenes.number	The number of highly varible genes. Default 2000
use.SingCellaR.varGenes	is logical. If TRUE, the highly variable genes identified by SingCellaR will be used.
k.anchor	Seurat's k anchor parameter. Default 5
k.filter	Seurat's k filter parameter. Default 200
k.score	Seurat's k score parameter. Default 30

supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.